Learning to read and write in evolution: From static pseudoenzymes and pseudosignalers to dynamic gear shifters

Abulikemu Abudukelimu, Thierry D.G.A. Mondeel, Matteo Barberis, Hans V. Westerhoff

Research output: Contribution to JournalReview articleAcademicpeer-review

Abstract

We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity. We identify functional pseudosignalers in the cyclin-dependent kinase complexes regulating cell-cycle progression. For the mitogen-activated protein kinase pathway, we illustrate how a 'dead' pseudosignaler could produce potentially selectable functionalities. Four billion years ago, bioenergetics may have shuffled 'electron-writers', producing various networks that all served the same function of anaerobic ATP synthesis and carbon assimilation from hydrogen and carbon dioxide, but at different ATP/acetate ratios. This would have enabled organisms to deal with variable challenges of energy need and substrate supply. The same principle might enable 'gear-shifting' in real time, by dynamically generating different pseudo-redox enzymes, reshuffling their coenzymes, and rerouting network fluxes. Non-stationary pH gradients in thermal vents together with similar such shuffling mechanisms may have produced a first selectable proton-motivated pyrophosphate synthase and subsequent ATP synthase. A combination of functionalities into enzymes, signalers, and the pseudoversions thereof may offer fitness in terms of plasticity, both in real time and in evolution.

Original languageEnglish
Pages (from-to)635-652
Number of pages18
JournalBiochemical Society Transactions
Volume45
Issue number3
DOIs
Publication statusPublished - 15 Jun 2017

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Gears
Adenosine Triphosphate
Learning
Proton-Motive Force
Systems Biology
Cyclin-Dependent Kinases
Genes
Nucleic Acid Repetitive Sequences
Coenzymes
Enzymes
Mitogen-Activated Protein Kinases
Ammonium Compounds
Ammonia
Carbon Dioxide
Energy Metabolism
Genetic Recombination
Oxidation-Reduction
Protons
Reading
Vents

Cite this

Abudukelimu, Abulikemu ; Mondeel, Thierry D.G.A. ; Barberis, Matteo ; Westerhoff, Hans V. / Learning to read and write in evolution : From static pseudoenzymes and pseudosignalers to dynamic gear shifters. In: Biochemical Society Transactions. 2017 ; Vol. 45, No. 3. pp. 635-652.
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Learning to read and write in evolution : From static pseudoenzymes and pseudosignalers to dynamic gear shifters. / Abudukelimu, Abulikemu; Mondeel, Thierry D.G.A.; Barberis, Matteo; Westerhoff, Hans V.

In: Biochemical Society Transactions, Vol. 45, No. 3, 15.06.2017, p. 635-652.

Research output: Contribution to JournalReview articleAcademicpeer-review

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AU - Abudukelimu, Abulikemu

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